scholarly journals Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 476 ◽  
Author(s):  
Shabina Iram ◽  
Muhammad Qasim Hayat ◽  
Muhammad Tahir ◽  
Alvina Gul ◽  
Abdullah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Cost Effective ◽  
Single Copy ◽  
Protein Coding ◽  
Important Species ◽  
Mutational Hotspots ◽  
Genome Features ◽  
Artemisia Scoparia ◽  
Chloroplast Genome Sequence

Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

scholarly journals The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1405
Author(s):  
Gurusamy Raman ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Gene Evolution ◽  
Single Copy ◽  
Specific Marker ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

scholarly journals Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1354
Author(s):  
Slimane Khayi ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Tatiana Tatusova ◽  
Abdelhamid El Mousadik ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Important Species ◽  
Complete Chloroplast Genome ◽  
Argania Spinosa ◽  
Protein Coding Genes ◽  
Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

scholarly journals Characterization of the complete chloroplast genome sequence and phylogenetic analysis of B. oleracea var. italica

2020 ◽  
Author(s):  
Zhenchao Zhang ◽  
Zhongliang Dai ◽  
Yuemei Yao ◽  
Yongfei Pan ◽  
Guosheng Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Genomic Structure ◽  
Gc Content ◽  
Single Copy ◽  
Biological Research ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Functional Components

Abstract Backgrounds: Broccoli (Brassica. oleracea var. italica L.) is known as one of the most nutritionally rich vegetables, as well as rich in functional components that benefit to health. The main purposes of this research were sequencing, assembling and annotation of chloroplast genome of broccoli based on Illumina HiSeq2500 sequencing platform. Results: The size of the broccoli cp genome is 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The GC content of the complete genome is 36.36%, while those of SSC, LSC, and IR are 29.1%, 34.15% and 42.35%, respectively. It harbors 134 functional genes, including 87 protein-coding genes, 39 tRNAs and 8 rRNAs, with 31 duplicates in the IRs. The most abundant amino acid in the protein-coding genes is leucine, while the least is cysteine. Codon usage frequency showed bias for A/T-ending codons in the cp genome. In the repeat structure analysis, a total of 34 repeat sequences and 291 simple sequence repeat (SSRs) were detected in the work. Although cp genomic structure and size are highly conserved, the SC-IR boundary regions are variable between the 7 cp genomes. The phylogenetic relationships based on complete cp genome from 9 species suggest that B. oleracea var. italica is closely related to Brassica juncea. Conclusions: The complete cp genome sequence was obtained and annotated for broccoli for the first time. The information acquired from this research will be useful for further species identification, population genetics and biological research of broccoli.

scholarly journals Complete chloroplast genome sequence of a vegetative Bermudagrass cultivar Tifeagle (Cynodon dactylon × Cynodon transvaalensis)

2019 ◽  
Vol 48 (4) ◽  
pp. 1083-1089
Author(s):  
Yancai Shi ◽  
Shaofeng Jiang ◽  
Shilian Huang
Keyword(s):  
Chloroplast Genome ◽  
Cynodon Dactylon ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Common Bermudagrass ◽  
Trampling Tolerance ◽  
Small Single Copy

Hybrid (Cynodonn dactylon × C. transvaalensis) is a widely distributed turfgrass and shows a great value of environment, horticulture and economic. Though, the chloroplast genome of C. dactylon has been reported, it might be helpful finding reasons that triploid bermudagrass shows a better drought and trampling tolerance than common bermudagrass through comparing chloroplast genome analysis. The present results showed the complete chloroplast genome of the C. dactylon × C. transvaalensis is 134655 bp in length. The tetramerous genome contained a large single copy (LSC) region (79,998 bp), a small single copy (SSC) region (12,517 bp), and a pair of inverted repeat (IR) regions (42,140 bp). In the chloroplast genome, 116 genes were predicted, including 83 protein-coding, 29 tRNA and 4 rRNA genes. Furthermore, a total of 80 repeat sequences were identified. Only 0.23% intergenicnon-collinear sequences were found between the chloroplast genome of Cynodon dactylon × C. transvaalensis and Cynodon dactylon.

scholarly journals Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7210 ◽  
Author(s):  
Wan Zhang ◽  
Yunlin Zhao ◽  
Guiyan Yang ◽  
Jiao Peng ◽  
Shuwen Chen ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Evolutionary History ◽  
Evolutionary Relationship ◽  
Hainan Island ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Phylogenetic Studies ◽  
Chloroplast Genome Sequence

Camellia oleiferais one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study usedC. oleiferathat was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies ofCamelliaplants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of HainanC. oleifera. The results showed that the whole chloroplast genome ofC. oleiferain Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of HainanC. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of HainanC. oleiferawere compared with mainlandC. oleiferaand those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of HainanC. oleifera, and allCamelliaplants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that HainanC. oleiferahad a similar evolutionary relationship withC. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.

scholarly journals Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Plant Evolution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Intergenic Regions ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

Abstract Background: The invasive alien species, Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, there are no extensive molecular studies for this plant. Results: Here, the complete chloroplast genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 bp and possessed quadripartite circular structure. The cp genome contained 115 unique genes, including 80 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Comparative analysis revealed that X. spinosum encoded a higher number of repeats (999 repeats) and 701 SSRs in their cp genome. Also, fourteen divergences (Pi > 0.03) were found in the intergenic regions. The accD gene underwent positive selection within Heliantheae, which contributes to further investigation of the adaptive plant evolution in the ecosystem. Additionally, the phylogenetic analysis revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and it is an early-diverging lineage of subtribe Ambrosiinae though it supports with very weak bootstrap value. Conclusion: The identified hotspot regions were thought to be useful molecular markers for resolving phylogenetic relationships and species validation of Xanthium.

scholarly journals Correction to: Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gurusamy Raman ◽  
Kyu Tae Park ◽  
Joo-Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Comparative Analyses ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248788
Author(s):  
Kyung-Ah Kim ◽  
Kyeong-Sik Cheon
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Illumina Miseq ◽  
Congeneric Species ◽  
Protein Coding ◽  
Important Species ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Miseq Platform ◽  
Chloroplast Genome Sequence

Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

scholarly journals Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6244 ◽  
Author(s):  
Simon Pfanzelt ◽  
Dirk C. Albach ◽  
K. Bernhard von Hagen
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Sequence Comparisons ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

scholarly journals Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242591
Author(s):  
Jie Li ◽  
Guang-ying Ye ◽  
Hai-lin Liu ◽  
Zai-hua Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Protein Coding ◽  
Important Species ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Mutational Hotspots

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

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